7L5L

Crystal structure of the DiB-RM protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Computational redesign of a fluorogen activating protein with Rosetta.

Bozhanova, N.G.Harp, J.M.Bender, B.J.Gavrikov, A.S.Gorbachev, D.A.Baranov, M.S.Mercado, C.B.Zhang, X.Lukyanov, K.A.Mishin, A.S.Meiler, J.

(2021) PLoS Comput Biol 17: e1009555-e1009555

  • DOI: https://doi.org/10.1371/journal.pcbi.1009555
  • Primary Citation of Related Structures:  
    7L5K, 7L5L, 7L5M

  • PubMed Abstract: 

    The use of unnatural fluorogenic molecules widely expands the pallet of available genetically encoded fluorescent imaging tools through the design of fluorogen activating proteins (FAPs). While there is already a handful of such probes available, each of them went through laborious cycles of in vitro screening and selection. Computational modeling approaches are evolving incredibly fast right now and are demonstrating great results in many applications, including de novo protein design. It suggests that the easier task of fine-tuning the fluorogen-binding properties of an already functional protein in silico should be readily achievable. To test this hypothesis, we used Rosetta for computational ligand docking followed by protein binding pocket redesign to further improve the previously described FAP DiB1 that is capable of binding to a BODIPY-like dye M739. Despite an inaccurate initial docking of the chromophore, the incorporated mutations nevertheless improved multiple photophysical parameters as well as the overall performance of the tag. The designed protein, DiB-RM, shows higher brightness, localization precision, and apparent photostability in protein-PAINT super-resolution imaging compared to its parental variant DiB1. Moreover, DiB-RM can be cleaved to obtain an efficient split system with enhanced performance compared to a parental DiB-split system. The possible reasons for the inaccurate ligand binding pose prediction and its consequence on the outcome of the design experiment are further discussed.


  • Organizational Affiliation

    Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lipocalin family protein
A, B
177Escherichia coliMutation(s): 7 
Gene Names: HGR07_10045HGR07_25230
UniProt
Find proteins for P0A901 (Escherichia coli (strain K12))
Explore P0A901 
Go to UniProtKB:  P0A901
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A901
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.97α = 90
b = 44.97β = 90
c = 158.65γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
xia2data scaling
PDB_EXTRACTdata extraction
xia2data reduction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM099842

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-27
    Type: Initial release
  • Version 1.1: 2021-11-24
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description